DNA mutations are inevitable. Despite proficient DNA repair mechanisms, somatic cells accumulate mutations during development and aging, generating cells with different genotypes within the same ...individual, a phenomenon known as somatic mosaicism. While the existence of somatic mosaicism has long been recognized, in the last five years, advances in sequencing have provided unprecedented resolution to characterize the extent and nature of somatic genetic variation. Collectively, these new studies are revealing a previously uncharacterized aging phenotype: the accumulation of clones with cancer driver mutations. Here, we summarize the most recent findings, which converge in the novel notion that cancer-associated mutations are prevalent in normal tissue and accumulate with aging.
Parkinson’s disease (PD) is a neurodegenerative disease caused by the loss of dopaminergic neurons in the substantia nigra. PARK2 mutations cause early-onset forms of PD. PARK2 encodes an E3 ...ubiquitin ligase, Parkin, that can selectively translocate to dysfunctional mitochondria to promote their removal by autophagy. However, Parkin knockout (KO) mice do not display signs of neurodegeneration. To assess Parkin function in vivo, we utilized a mouse model that accumulates dysfunctional mitochondria caused by an accelerated generation of mtDNA mutations (Mutator mice). In the absence of Parkin, dopaminergic neurons in Mutator mice degenerated causing an L-DOPA reversible motor deficit. Other neuronal populations were unaffected. Phosphorylated ubiquitin was increased in the brains of Mutator mice, indicating PINK1-Parkin activation. Parkin loss caused mitochondrial dysfunction and affected the pathogenicity but not the levels of mtDNA somatic mutations. A systemic loss of Parkin synergizes with mitochondrial dysfunction causing dopaminergic neuron death modeling PD pathogenic processes.
•Parkin preferentially protects dopaminergic neurons from mitochondrial stress•Phosphorylated-S65 ubiquitin is increased in the brain after mitochondrial stress•Parkin affects the pathogenicity not quantity of somatic mtDNA point mutations•Loss of Parkin exacerbates mitochondrial dysfunction in neurons
Recessive mutations in Parkin contribute to Parkinson’s disease. Pickrell and Huang et al. use a mouse model to discover endogenous Parkin preferentially protects dopaminergic neurons from mitochondrial dysfunction.
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► Electrospinning is a particularly low-cost and versatile method for manufacturing nanofibers. ► Electrospun materials have applications in fuel cells, solar cells and lithium-ion ...batteries. ► Membranes with high surface areas have unique material properties that can advance the development of energy related devices.
The tasks of harvesting, transmitting, and storing the energy required to meet global demands are some of the most pressing needs we will face in the near future. Scientists are seeking new technologies to generate renewable and clean energy resources. Nanofiberous materials with high surface areas and porosities have attracted significant attention in recent years and are considered to be promising candidates to address these critical issues. Nanofibers can be produced by many techniques. Of these, electrospinning is a particularly low cost and versatile method. This paper highlights research into the use of electrospinning to create materials suited for four major energy-related applications: (1) fuel cells, (2) dye-sensitized solar cells, (3) Li-ion batteries, and (4) supercapacitors. In addition, electrospun nanofibers used in other areas, such as thermoelectrical and piezoelectric materials, are also discussed. Specific attention is given to the material properties that have been achieved through electrospinning and what limitations of existing processes offer opportunities for future research.
Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been ...difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >10(7) wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ~5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G → T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G → A and T → C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA.
In modern power systems and electricity markets, demand response (DR) programs play an important role enabling the mitigation of critical load periods or price-peaking scenarios, thereby improving ...system reliability. Price fluctuations, in forward or real-time markets, can be an effective price-based DR mechanism for curtailing or shifting load. However, using dynamic pricing to achieve a desired load profile requires both an accurate demand forecast and knowledge of the price elasticity of demand, which is notoriously difficult to estimate. The limited accuracy of these parameter estimates is the main source of uncertainty limiting appropriate DR implementation. In this paper, we present a novel DR scheme that avoids the need to predict the price elasticity of demand or demand forecast, yet still delivers a significant DR. This is done based on the consumers' submissions of candidate load profiles ranked in the preference order. The load aggregator then performs the final selection of individual load profiles subject to the total system cost minimization. Additionally, the proposed DR model incorporates a fair billing mechanism that is enhanced with an ex post consumer performance tracking scheme implemented in a context of a virtual power plant aggregating load and generation units.
The animal germline is an immortal cell lineage that gives rise to eggs and/or sperm each generation. Fusion of an egg and sperm, or fertilization, sets off a cascade of developmental events capable ...of producing an array of different cell types and body plans. How germ cells develop, function, and eventually give rise to entirely new organisms is an important question in biology. A growing body of evidence suggests that phase separation events likely play a significant and multifaceted role in germ cells and development. Here, we discuss the organization, dynamics, and potential functions of phase-separated compartments in germ cells and examine the various ways in which phase separation might contribute to the development of multicellular organisms.
Phase separation is a versatile and widespread biophysical phenomenon that contributes to subcellular organization, gene regulation, environmental sensing, and a variety of other cellular processes. Dodson and Kennedy review how animals regulate and exploit the properties of phase separation in the germline and during development.
Next-generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA ...sequence in a single experiment, the error rate of ∼1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, we have developed a method termed Duplex Sequencing. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors result in mutations in only one strand and can thus be discounted as technical error. We determine that Duplex Sequencing has a theoretical background error rate of less than one artifactual mutation per billion nucleotides sequenced. In addition, we establish that detection of mutations present in only one of the two strands of duplex DNA can be used to identify sites of DNA damage. We apply the method to directly assess the frequency and pattern of random mutations in mitochondrial DNA from human cells.
The accumulation of somatic mitochondrial DNA (mtDNA) mutations is implicated in aging and common diseases of the elderly, including cancer and neurodegenerative disease. However, the mechanisms that ...influence the frequency of somatic mtDNA mutations are poorly understood. To develop a simple invertebrate model system to address this matter, we used the Random Mutation Capture (RMC) assay to characterize the age-dependent frequency and distribution of mtDNA mutations in the fruit fly Drosophila melanogaster. Because oxidative stress is a major suspect in the age-dependent accumulation of somatic mtDNA mutations, we also used the RMC assay to explore the influence of oxidative stress on the somatic mtDNA mutation frequency. We found that many of the features associated with mtDNA mutations in vertebrates are conserved in Drosophila, including a comparable somatic mtDNA mutation frequency (∼10(-5)), an increased frequency of mtDNA mutations with age, and a prevalence of transition mutations. Only a small fraction of the mtDNA mutations detected in young or old animals were G∶C to T∶A transversions, a signature of oxidative damage, and loss-of-function mutations in the mitochondrial superoxide dismutase, Sod2, had no detectable influence on the somatic mtDNA mutation frequency. Moreover, a loss-of-function mutation in Ogg1, which encodes a DNA repair enzyme that removes oxidatively damaged deoxyguanosine residues (8-hydroxy-2'-deoxyguanosine), did not significantly influence the somatic mtDNA mutation frequency of Sod2 mutants. Together, these findings indicate that oxidative stress is not a major cause of somatic mtDNA mutations. Our data instead suggests that somatic mtDNA mutations arise primarily from errors that occur during mtDNA replication. Further studies using Drosophila should aid in the identification of factors that influence the frequency of somatic mtDNA mutations.
The development of new RNA‐binding ligands is attracting increasing interest in fundamental science and the pharmaceutical industry. The goal of this study was to improve the RNA binding properties ...of triplex‐forming peptide nucleic acids (PNAs) by further increasing the pKa of 2‐aminopyridine (M). Protonation of M was the key for enabling triplex formation at physiological pH in earlier studies. Substitution on M by an electron‐donating 4‐methoxy substituent resulted in slight destabilization of the PNA–dsRNA triplex, contrary to the expected stabilization due to more favorable protonation. To explain this unexpected result, the first NMR structural studies were performed on an M‐modified PNA–dsRNA triplex which, combined with computational modeling identified unfavorable steric and electrostatic repulsion between the 4‐methoxy group of M and the oxygen of the carbonyl group connecting the adjacent nucleobase to PNA backbone. The structural studies also provided insights into hydrogen‐bonding interactions that might be responsible for the high affinity and unusual RNA‐binding preference of PNAs.
RNA binding improved: A 2‐aminopyridine (M) nucleobase enables strong and selective triple helical binding of peptide nucleic acid (PNA) to dsRNA. However, further modification of M with the electron‐donating 4‐methoxy group did not enhance the binding affinity. NMR structural studies showed that this is likely due to steric and electronic repulsion (denoted by the red spheres) between the oxygen of 4‐methoxy group and the oxygen of the carbonyl connecting the adjacent PNA nucleobase to the PNA backbone.
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